A universal framework to efficiently share material and process resources in the DNA construction world

TL;DR

This paper introduces QUEEN, an open-source framework that standardizes and automates the sharing and reproducibility of DNA construction processes and resources, enhancing efficiency and collaboration in synthetic biology.

Contribution

QUEEN provides a novel, flexible, and compatible system for designing, sharing, and reproducing DNA constructs using standardized GenBank files, addressing current manual and non-reproducible practices.

Findings

QUEEN enables automated regeneration of DNA construction processes.

The framework improves resource sharing and reproducibility in DNA design.

QUEEN-compatible files integrate with existing DNA repositories.

Abstract

DNA constructs and their annotated sequence maps have been rapidly accumulating with the advancement of DNA cloning, synthesis, and assembly methods. Such a resource has the potential to be optimally utilized in an autonomous DNA building platform. However, most DNA design processes today remain manually operated with the assistance of graphical user interface (GUI) software. Furthermore, as seen commonly in the life sciences, reproducibility of DNA construction process descriptions is usually not guaranteed, and utilization of previously developed materials and protocols is not appropriately credited. Here, we developed an open-source process description and resource sharing framework QUEEN (a framework to generate quinable and efficiently editable nucleotide sequence resources) to resolve these issues in building DNA. QUEEN enables the flexible design of new DNA by using existing DNA resource files and recoding the construction process in an output file (GenBank file format). The GenBank files generated by QUEEN are able to regenerate the process codes that perfectly clone themselves and bequeath the design history to successive DNA constructs that recycle their partial resources. QUEEN-generated GenBank files are compatible with the existing DNA repository services and software. We propose QUEEN as a solution to start significantly advancing our material and protocol sharing of DNA resources.